Abstract Manufactured metal (oxide) nanoparticles are entering the aquatic environment with little understanding on their potential health impacts for exposed organisms. Adopting an integrative approach, we investigated effects of particle size and coating on biological responses for two of the most commonly used metal (oxide) nanoscale particles, silver (Ag) and titanium dioxide (TiO2) in zebrafish embryos. Titanium dioxide nanoparticles (nominally, 4nm, 10nm, 30nm and 134 nm) had little or no toxicity on the endpoints measured. Ag both in nano form (10nm and 35nm) and its larger counterpart (600-1600 nm) induced dose dependent lethality and morphological defects, occurring predominantly during gastrula stage. Of the silver material tested 10nm nanoparticles appeared to be the most toxic. Coating Ag nanoparticles with citrate or fulvic acid decreased toxicity significantly. In-situ hybridisation analysis identified the yolk syncitial layer (YSL) as a target tissue for Ag-nano toxicity where there was a significant induction of the heavy metal stress response gene, metallothionein 2 (Mt2) at sub-lethal exposures. Coherent Anti-stroke Raman Scattering (CARS) microscopy provided no evidence for silver particles crossing the chorionic membrane in exposed embryos. Collectively, our data suggest that silver ions play a major role in the toxicity of Ag nanoparticles.